A mathematical model was used to derive equations to examine incorporation into and half-lives of long chain fatty acids within brain phospholipids in vivo . In rats, the model was combined with quantitative autoradiography and biochemical analysis using as intravenous tracers saturated [9,10-3H]palmitic acid ([3H]PAM) and polyunsaturated [1-14C]arachidonic acid ([14C]AA) and [1-14C]docosahexaenoate acid ([14C]DHA). Half-lives could be determined using a new high-pressure liquid chromatography method to measure specific activity relative to plasma fatty acid specific activity of brain acyl-CoA species. Low values for this dilution factor indicate marked recycling of fatty acids within phospholipids (half-life of about 1 h for arachidonate). Recycling of polyunsaturated fatty acids reflects activity of phospholipase A2 in signal transduction, and could be inhibited by manoalide, an inhibitor of this enzyme, as well as chronic lithium. Labeled arachidonate and docosahexaenoate but not labeled palmitate, are incorporated into synaptic phospholipids during activation by the cholinergic agonist arecoline, indicating that the fatty acid method images signal transduction at synapses. Ischemia releases free fatty acids from brain phospholipids due to phospholipase activation, and increases arachidonoyl-CoA, but not other acyl-CoA concentrations (total pool is unchanged). Thus, recovery from ischemia is rate-limited by reacylation into lysophospholipids through the acyl-CoA pool. Chronic visual deprivation is associated with reduced membrane remodeling, measured by reduced incorporation of labeled fatty acids into central visual structures. On the other hand, kindling in rats caused by unilateral amygdala stimulation is associated with increased membrane remodeling in ipsilateral thalamic and amygdala nuclei, and increased incorporation of [3H]PAM. Increased incorporation of [3H]PAM also occurs ipsilateral to a chronic lesion of the nucleus basalis in rats, which is also consistent with increased membrane remodeling. The fatty acid method was extended to monkeys following the synthesis of positron-emitting fatty acids labeled with carbon-11 when using positron emission tomography (PET).